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Objectives

Introduction to Perl & Bioperl (I)

Basic Perl Programming

Xuefeng Zhao

L. H. Baker Center, ISU

• Get an overview of basic Perl

programming

• Write simple perl scripts to manipulate

DNA/RNA sequences

BCB 444/544X

Outline

Why Perl?

•

Why Perl?

Install Perl/Bioperl on Windows

Run a Hello perl script

Data Types, Variables and Built-in Functions

Control Structures

Basic IO

Subroutines & Functions

More String Manipulation

• Perl: Practical Extraction and Report Language

•

Easy to learn

Good for string manipulation and File IO

Open source for all OS’s

A lot of Bioinformatics tools available

Install Perl/Bioperl

Ref: Install Note on www.bioperl.org

1. Unix/Linux: Pre-installed

2. Mac: http://www.macperl.org

3. Windows

Download the current ActivePerl from

www.activeperl.com.

The windows

installer package file is ActivePerl-5.8.6.811-MSWin32-x86-122208.msi

– Install ActivePerl using the default values by double-clicking the msi file, using

c:\perl as the Perl home

– *** To install GD.pm.

ppm> install

http://theoryx5.uwinnipeg.ca/ppms/GD.ppd

– To install Bioperl

ppm>rep add Bioperl

http://bioperl.org/DIST

ppm>search bioperl

1. bioperl

2. bioperl

…

8. bioperl-1.4

….

[1.2.3] bioinformatics tool kits

[1.2.1] non

[1.4] BioPerl 1.4 PPM3 Archive

Run a Hello Perl script

•

Download all Perl scripts for the class from

www.bioinformatics.iastate.edu/BBSI/

to your USB disk, and run hello.pl

To run:

perl hello.pl

To run:

hello.pl

Script:Hello.pl

#!/usr/local/bin/perl

#hello perl script

use strict;

print "Hello, ISU-BCBSI\n";

Basic Syntax:

1. the first #! line indicates the location of perl, used for Unix/Linux OS.

2. Free form, case-sensitive

3. Each statement ends with a semicolon (;)

4. A comment line starts with a pound sign (#), you have to comment line by

line.

ppm>install 8

…….

Successfully installed Bioperl-1.4 version 1.4 in ActivePerl 5.8.6.811

Data type, Variables and Built in functions

Data Types:

1. Scalar: string and number.

2. Array: list arrays (array) and associative arrays(hash).

Variables:

1. Scalar variables: start with $.

Ex.

$DNAstr, $numNT

2. Array: start with @.

Ex.

@nameAA

3. Hash: start with %.

Ex.

%RestricteEnzym

Some Perl built-in functions:

length

substr index

push

pop

keys

open

die

exit

Scalar variables: number and string

Number: $numVar=EXPRESSION;

$counter=20;

$Tm=37.5;

String variables: $strVar=EXPRESSION;

#using single quote(‘), no variable expansion takes place,

$str1=‘isu-bcbsi’ ;

$strSupport=‘$$$:NIH-NSF’;

# $strSupport: $$$:NIH-NSF

#using double quote(“), a variable expansion takes place,

#sepcial characters needs to be escape-ed

$str2=“$str1, ames, iowa’ ;

# $str2: “isu-bcbsi, ames, iowa”;

#using backstick(`), the variable is assigned the return values from the command

# line

$strDateNow=`date /t`;

# $strDateNow: “Mon 06/06/2005”

rindex

sort

Operators and Functions for Scalar variables

Arithmetic Operators: =, +, -, *, /, %, **

Array

Array:

Notation: $counter++; $counter= $counter+1; $counter += 1;

$counter--; $counter= $counter-1; $counter -= 1;

Operator and function for strings

Operator/Function

Dot (.)

Example

$str1=“DNA”;

$str2=“RNA”;

$str3=$str1.” and ”.$str2;

$str1 .= $str2;

$len=length(“ACGT”)

$idx=index(“ACGTACGT”, “C”);

$ridx=index(“ACGTACGT”, “C”);

Desc

Concatenation:

$str3: DNA and RNA

Appending:

$str1: DNARNA

$len: 4

$idx: 1

$ridx: 5

$msubstr: GTA

$str1: DN

@NTlist = (“A”,”T”,”G”,”C”);

# assign 4 elements to the array, included in ();

$nt_2 = $NTlist[1];

# the array index starts 0, the index number is include in [];

$last_idx = $#NTlist;

# last_idx: 3

$num_ele = scalar @

NTlist; # num_element: 4

Operator/Function

push(@arr, element)

pop(@arr)

shift(@arr)

unshift(@arr, element)

delete($arr[$idx])

Example

push (@NTlist, (“A”,”T”)):

$m_nt= pop(@NTlist);

shift((@NTlist)

unshift((@NTlist, “G”);

delete $NTlist[1];

Desc

@NTlist: A, T, G, C, A, T

$m_nt: T;

@NTlist: A, T, G, C, A

@NTlist: T, G, C, A

@NTlist: G, T, G, C, A

@NTlist: G, G, C, A

length(

STRING)

index(

STRING,SEARCH)

rindex(

STRING,SEARCH)

LEN, REPLACEMENT

)

substr(

STRING,OFFSET,

$msubstr=substr(“ACGTACGT”, 2,

3);

chop(

STRING)

chomp(

STRING)

$str1=“DNA”;

chop($str1);

#matching chop, remove “\n”;

chomp($str1);

Hash

# indexed by strings. Brace {} for key, percent sign % for entire array

# assign 4 elements to the array,

%AAlist=(Ala=>”A”,

Gly=>”G”,His=>”H”, Phe=>”F”);

$aa_gly=$AAlis{Gly};

Operator/function

keys(%ARRAY)

values(%ARRAY)

each(%ARRAY)

delete($ARRAY{KEY})

example

@aa_keys=keys (%AAlist);

@aa_vals=values (%AAlist);

each((%AAlist)

delete($AAlist{Ala});

$AAlis{Val}=“V”;

Desc

@aa_keys: Ala,Gly,His,Phe

Not ordered

@aa_vals: A, G, H, F,

Not ordered

Return pair by pair (key, value)

=>(Ala, A), used for loop

Remove the pair(Ala, A)

Add one element

Control Structures: IF

If (condition){

statements;….

}

elsif {

statements;….

}

else {

statements;….

}

E - ESE

LSIF L

If (condition){

statements

;….

}

#use if only

If (condition){

statements;….

}

elsif {

statements;….

}

#use elsif only, no switch in

Perl, use elsif to get around

comparison

Great than

Great than or equal

Equal

Less than

Less or equal

Not equal

Comparison returns -1,0,1

number

<=>

string

cmp

Loop Structures: WHILE,DO

Control Structures:IF

E - ESE

LSIF L

-- WHILE Loop

while (condition){

statements;….

}

-- DO-WHILE Loop:

do at least once

Do{

statements;….

}while(condition)

-- FOR Loop

For (initial values; test; increment)

{ statement;

}

HILE, FOR

If ($m_nt eq “A”) { $num_A++; }

elsif

($m_nt eq “T”) { $num_T++; }

# A counter

# T counter

elsif ($m_nt eq “G”){ $num_G++; } # G counter

elsif ($m_nt eq “C”){ $num_C++; }

else {

$num_error++; }

#C counter

# error

Two control statements for loop:

last

Declare that this is the last statement in the

loop

Start a new iteration of the loop

Basic IO

Input

Keyboard (STDIN)

file

$m_input=<STDIN>;

# wait for the input unt the new line character

Open(MYFILEHANDLE, “<mySeqFileName”):

@all_lines=<MYFILEHANDLE>;

Close(MYFILEHANDLE);

print STDOUT “Hello, ISU-BCBSI class!”;

print “Hello, ISU-BCBSI class!”;

Open(MYFILEHANDLE, “>mySeqFileName”);

print MYFILEHANDLE $m_line;

Close(MYFILEHANDLE);

GC_counter.pl

Write a perl script to count GC content in a DNA sequence

Output

Screen

Output

File

File IO

| CMD

CMD |

Desc

read

write

read and write

append

open a pipe to CMD

open a pipe from CMD

File Test Operator

-r

-x

-e

-d

desc

readable

executable

exists

a directory?

Subroutine & Functions

1. No difference for subroutine and functions in perl. Use subroutine all the time.

2. How to call sub: & is used before the sub name

3. Arguments are passed in the subroutine by a special array @_.

Out2File_FASTA.pl

#demo calls subroutine

$g_msg=“calling from outside”;

&get_msg($g_msg);

print $g_msg, “\n”;

Output the DNA sequence to a file in

FASTA format. The FASTA format description is:

http://ngfnblast.gbf.de/docs/fasta.html

sub get_msg()

{

$m_msg= $_[0];

# Arguments are listed in @_

print $m_msg, “\n”;

$g_msg =“hello from sub”; # the global variable is updated here!!!! Scope issue

}

Anti-bugging

#all variables must be declared before being used.

use strict;

# give warning msg

use warnings;

# a little bit more info than use warnings

use diagnostics;

# Limit the scope of variables

my(): lexical scope, visible in the scope of the current block that defines it

only.

local(): does not create a private variable, but let the global variable has

a temp value and be restored to the old values when the variable is

out of scope.

debugging

1. print out or comment out

2 run perl debugger

perl -d your script.pl

db> h

db>n # next step

db> x $your_var # to exam the value

More String Manipulation:split, match & regular expression

Ref Ch7, by Michael Moorhouse and Paul Barry

Split:

$NTStr = “A:T:G:C";

@NTlist= split(/:/, $NTStr );

summary

Matching:

$NTStr=“ATGCAAAAAAA”;

$NTStr =~ /GC/;

Substitute:

$NTStr=“ATGCAAAAAAA”;

$NTStr =~ s/AAA/A/

Translation: character-by-character

translation

$NTStr = “ATGCAAAAAAA”;

$NTStr =~ tr/ATGC/TACG/ ;

Data Types, Variables and Operations

Control Structures

Basic IO

Subroutines & Functions

More String Manipulation

Debug

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